In chemistry, molecular recognition is a phenomenon in which molecules are distinguished accurately from other molecules. Chemically, it indicates that certain molecules abnormally bond with other molecules (or the same species). This phenomenon involves three-dimensional interactions among molecules connected with hydrogen bonds, hydrophobicity interactions, ionic interaction, or other noncovalent bond interactions. It is thought that sources of molecular recognition include molecular solid structures and electronic configurations.

Molecular recognition is a new field dating to 1967, when C. J. Pedersen found crown ether. Molecular recognition chemistry is also called host-guest chemistry, and at present it is usually categorized as supramolecular chemistry amalgamated with molecular histochemistry . Specific examples of molecular recognition include systems in which hydrophobic molecules are included in cyclodextrin as well as the interaction between crown ether and alkali metals.

Molecular recognition consists of static molecular recognition and dynamic molecular recognition.

Static molecular recognition is likened to the interaction between a key and a keyhole; it is a 1:1 type complexation reaction between a host molecule and a guest molecule. To achieve advanced static molecular recognition, it is nessessary to make recognition sites that are suitable for guest molecules.

Dynamic molecular recognition is a molecular recognition reaction that dynamically changes the equilibrium to an n:m type host-guest complex by a recognition guest molecule (see figure). There are some equivalents by the combination of host molecules. Both static molecular recognition and dynamic molecular recognition by metal ions are observed in the case of molecular recognition between crown ether complex and alkali metal ion.

Dynamic molecular recognition appearing in supramolecules is essential for designing highly functional chemical sensors and molecular devices . The quest for understanding this principle and its functions is now an important issue.